CHY 431 Biological Chemistry Structure Determination by NMR CHY 431 Biological Chemistry Karl D. Bishop, Ph.D. Lecture 1 - Introduction to NMR Lecture 2 - 2D NMR, resonance assignments Lecture 3 - Structural constraints, 3D structure calculation

Structure Determination by NMR Biological molecules such as proteins and nucleic acids can be large and complex. They can easily exceed 2000 atoms. Knowing their structure is critical in understanding the relationship between structure and function. X-ray crystallography is an excellent method to determine detailed 3D structures of even some of the largest biological molecules. However, it has some significant difficulties. Getting crystals and is the structure biologically relevant. NMR can be used to determine 3D structure and dynamics in solution! It’s limitation is molecular size. However, this is changing. A good online book about basic NMR is at http://www.cis.rit.edu/htbooks/nmr/

TATA Box Binding Protein Bound to DNA Duplex 2071 atoms 2175 bonds

NMR Structure Determination What is NMR? How does NMR work? How is a three dimensional structure elucidated?

Nuclear Magnetic Resonance Nuclear spin m = g I h m - magnetic moment g - gyromagnetic ratio I - spin quantum number h - Planck’s constant I is a property of the nucleus Mass # Atomic # I Odd Even or odd 1/2, 3/2, 5/2,… Even Even 0 Even Odd 1, 2, 3 m As an exercise determine I for each of the following 12C, 13C, 1H, 2H, 15N .

Apply an external magnetic field (i.e., put your sample in the magnet) z w = g Bo = n/2p w - resonance frequency in radians per second, also called Larmor frequency n - resonance frequency in cycles per second, Hz g - gyromagnetic ratio Bo - external magnetic field (the magnet) w m Bo m Spin 1/2 nuclei will have two orientations in a magnetic field +1/2 and -1/2. w

Net magnetic moment z w m +1/2 Bo -1/2 m w

Ensemble of Nuclear Spins Bo Bo > 0 Bo = 0 Randomly oriented Highly oriented N S Each nucleus behaves like a bar magnet.

The net magnetization vector w w z one nucleus x Mo - net magnetization vector allows us to look at system as a whole many nuclei z w z y y x x

Allowed Energy States for a Spin 1/2 System DE = g h Bo = h n antiparallel -1/2 E DE +1/2 parallel Bo = 0 Bo > 0 Therefore, the nuclei will absorb light with energy DE resulting in a change of the spin states.

Energy of Interaction DE = g h Bo = h n n = g Bo/2p The frequency, n, corresponds to light in the radiofrequency range when Bo is in the Teslas. This means that the nuclei should be able to absorb light with frequencies in the range of 10’s to 100’s of megaherz. Note: FM radio frequency range is from ~88MHz to 108MHz. 77Se, g = 5.12x107 rad sec-1 T-1 n = g Bo/2p

Nuclear Spin Dynamics Mo Mo Mo RF on RF off RF off z z z Mo y y y x x x RF on RF off RF off Effect of a 90o x pulse

Nuclear Spin Evolution z z z Mo y y y w x x x Mo x RF receivers pick up the signals I Time y

Free Induction Decay FT The signals decay away due to interactions with the surroundings. A free induction decay, FID, is the result. Fourier transformation, FT, of this time domain signal produces a frequency domain signal. FT Frequency Time

Spin Relaxation There are two primary causes of spin relaxation: Spin - lattice relaxation, T1, longitudinal relaxation. Spin - spin relaxation, T2, transverse relaxation. lattice

Nuclear Overhauser Effect Caused by dipolar coupling between nuclei. The local field at one nucleus is affected by the presence of another nucleus. The result is a mutual modulation of resonance frequencies. N S N S

Nuclear Overhauser Effect The intensity of the interaction is a function of the distance between the nuclei according to the following equation. I - intensity A - scaling constant r - internuclear distance I = A (1/r6) r1,2 Arrows denote cross relaxation pathways r1,2 - distance between protons 1 and 2 r2,3 - distance between protons 2 and 3 1H 1H 1 2 r1,3 r2,3 The NOE provides a link between an experimentally measurable quantity, I, and internuclear distance. NOE is only observed up to ~5Å. 1H 3

Scalar J Coupling Electrons have a magnetic moment and are spin 1/2 particles. J coupling is facilitated by the electrons in the bonds separating the two nuclei. This through-bond interaction results in splitting of the nuclei into 2I + 1states. Thus, for a spin 1/2 nucleus the NMR lines are split into 2(1/2) + 1 = 2 states. Multiplet = 2nI + 1 n - number of identical adjacent nuclei I - spin quantum number 1H 1H 12C 12C

Scalar J Coupling The magnitude of the J coupling is dictated by the torsion angle between the two coupling nuclei according to the Karplus equation. J = A + Bcos(q) + C cos2(q) A = 1.9, B = -1.4, C = 6.4 C H q Karplus Relation 3J A, B and C on the substituent electronegativity. q

Torsion Angles Coupling constants can be measured from NMR data. Therefore, from this experimental data we can use the Karplus relation to determine the torsion angles, q. Coupling constants can be measured between most spin 1/2 nuclei of biological importance, 1H, 13C, 15N, 31P The most significant limitation is usually sensitivity, S/N.

Chemical Shift, d The chemical is the most basic of measurements in NMR. The Larmor frequency of a nucleus is a direct result of the nucleus, applied magnetic field and the local environment. If a nucleus is shielded from the applied field there is a net reduction if the magnetic field experienced by the nucleus which results in a lower Larmor frequency. d is defined in parts per million, ppm. d = (w - wo)/wo * 106

Biomolecular NMR Experiments J Correlated Based Experiments COSY - Correlated Spectroscopy 2QF-COSY - Double Quantum Filtered Spectroscopy HETCOR - Heteronuclear Correlated Spectroscopy E.COSY - Exclusive COSY HOHAHA - Homonuclear Hartmann Hahn (TOCSY) Nuclear Overhauser Based Experiments NOESY - Nuclear Overhauser Effect Spectroscopy ROESY - Rotating Frame Overhauser Effect Spectroscopy Three Dimensional Experiments Use a Combination NOESY - TOCSY NOESY - NOESY

Summary There are three primary NMR tools used to obtain structural information Nuclear Overhauser effect - internuclear distances J Coupling - torsion angles Chemical shift - local nuclear environment (Chemical exchange can also be monitored by NMR.)